Michael Garibaldi enters C'n'C looking for Captain Sheridan and Commander Ivanova. David Corwin explains that Sheridan had Ivanova take him to Bay 13, which surprises Garibaldi. Bay 13 is reserved exclusively for Ambassador Kosh' transport ship. Sheridan inspects the ship with Ivanova, marveling at how advanced the Vorlons must be. When he steps too close, he is warned away by the ship's security system. Ivanova explains that they had to cordon off the bay to everyone because the maintenance workers who used to be assigned to the Bay kept claiming that the ship "talked to them" in their sleep. Sheridan decides the time has come to learn more about Kosh and the Vorlon Empire. They are interrupted by Garibaldi, who asks to speak to them (privately, and away from the ship). After they leave, Kosh emerges from a hiding place nearby and communicates something with the ship.

In Sheridan's office, Garibaldi explains that Dr. Everett Jacobs, the personal physician to the President, is allegedly on the run, having stolen top secret data with the intention of defecting to an alien power. Garibaldi explains that Earthforce has just alerted him that the doctor is supposedly on the station – and their orders are shoot to kill.

Derek Cranston, of Earthforce Special Intelligence, soon arrives with a small detachment to help coordinate the search for Jacobs. Cranston warns that the information Jacobs stole could shake the very foundations of the Earth Alliance. Sheridan agrees to fully cooperate with the search.

Garibaldi starts his own search with Dr. Franklin, aware that Franklin studied under Jacobs at Harvard University. Franklin flat out refuses to believe Jacobs is guilty of treason, espionage, or any other charge.

In a market in Downbelow, Jacobs approaches a Merchant, hoping to acquire an Identicard. The merchant becomes alarmed at how eager Jacobs wants it and refuses to deal with him, leaving a distraught Jacobs to wander away. He is noticed by a man nearby.

Sheridan passes Kosh in the hallways and decides to approach him. He offers to spend some time with Kosh, hoping to "build some bridges." Sheridan also confronts Kosh about entering his dreams while he was captured by the Streib. Kosh only says that he entered Sheridan's mind seeking understanding.

Cranston briefs Security on the search. Zack Allan speaks up, pointing out that a full search of the station could take months. Cranston explains that Dr. Jacobs, like all high ranking personnel of EarthGov, has been "tagged" by an electronic device that emits a low level signal. The signal has a short range, but should help them cut down the search time by the use of hand scanners.

As Garibaldi and Sheridan walk through the station, discussing the search, Sheridan suddenly notices a ribbon tied to a bulkhead. He quickly excuses himself and heads for a secluded area nearby. There he meets Sarah, someone sent by General William Hague, who warns Sheridan that he is in great danger.

Sarah explains that Jacobs is no traitor, but rather a direct threat to President Clark. As Earthforce Special Intelligence is under the President's direct control, he is using that organ to try and eliminate the threat. Sarah explains that Clark disembarked Earthforce One 24 hours before it exploded (killing President Luis Santiago) alleging he was sick. Dr. Jacobs, as the attending physician, has proof otherwise – which implies Clark knew the ship would explode. Sarah explains that her people helped Jacobs escaped Earth, but their plans went awry and now he's trapped on the station. She insists he help Jacobs escape by any means possible. Sheridan immediately links Garibaldi and tells him to meet him in his quarters.

In Medlab, Dr. Franklin gets a coded message from Garibaldi telling him to meet him at his place in civilian dress as soon as possible.

In Downbelow, Dr. Jacobs takes some Stims and records a message to his wife, though he has to cut it short when security guards close in. He is able to evade them, however.

Garibaldi explains that the two of them will go into Downbelow undercover looking for Jacobs. He wants Franklin to come along since Franklin knows the doctor better than anyone on the station and will hopefully be able to help track him down.

Dr. Jacobs is confronted by two underworld thugs, Max and Chase, who have noticed how much Jacobs obviously stands out in Downbelow. Believing him to be valuable (one way or another), Max draws a knife and insists the doctor "will pay."

Max and Chase hold Jacobs in a secured spot nearby. Max searches the doctor's coat and finds a data crystal which he pockets. He also finds an antique watch engraved with the seal of the Earth Alliance President. Max orders Chase to watch the doctor while he goes to investigate who the doctor is.

Cranston discusses the course of the investigation with Sheridan and Ivanova, explaining that he believes Jacobs is somewhere in Downbelow. Sheridan suggests he might actually be "downtown," a part of between Blue Sector and Grey Sector between the hull and the water reclamation systems. Cranston jumps on this suggestion, ordering his teams to investigate it immediately. After he leaves, Ivanova states how amused she is by the captain's diversion, as the place he has sent the search team contains no less than 47 pressure doors, each welded shut, not including the two big ones on either side of the waste treatment facility. As they talk, Sheridan is informed that Kosh has just requested his presence in his quarters. Both Sheridan and Ivanova are shocked, as Kosh has never asked to see anyone before, and Sheridan quickly decides to make the meeting.

Garibaldi and Franklin continue their exhausting search through Downbelow. They pause to rest and eat some food. While they eat, Franklin discusses how he knew Jacobs back in school, back in the time shortly after the Dilgar War when Humans were a lot more optimistic about space. Suddenly, Franklin notices a merchant trying to sell Jacobs' antique watch. They lean on the merchant, asking where he got the watch.

Meanwhile, Max contacts Cranston via the Babcom. Max implies that he has Jacobs, but asks for a finder's fee of 10,000 credits. Cranston agrees, and Max explains that he will contact him again when he is ready to make the exchange.

Sheridan visits Kosh in his quarters. He mentions that "everyone" would like to see what Kosh looks like beneath his Encounter suit, but Kosh replies that "they are not ready; they would not understand." He also says that Sheridan is not ready, not even understanding himself. The Vorlon seems to get frustrated by Sheridan and asks him to leave. Sheridan angrily confronts him about his behavior: he says he thinks Kosh has been watching him ever since he arrived, and again asks about how Kosh touched his mind when he was captured. When he finally asks, "What do you want?" Kosh angrily tells him to never ask that question. Finally, Kosh agrees to "teach" Sheridan, until he is ready "to fight legends."

Garibaldi and Franklin storm the area that Chase is holding Jacobs. The thug stabs Garibaldi in the arm, but they are able to knock him out and free Jacobs. The doctor explains that Max stole his data crystal, which contains copies of all his examinations of the President. Garibaldi orders Franklin to hide nearby with Jacobs while he gets the crystal back from Max.

Max returns soon afterward and finds Chase tied up and Garibaldi waiting for him. After Garibaldi fires a few warning shots, Max timidly hands over the data crystal.

Cranston confronts Sheridan about failing to disclose that they can use the station's scanners to search for Jacob's signal. Ivanova interrupts, calling away Sheridan on an emergency. She remains with Cranston, explaining that it will take a couple of hours to get the station wide scanner aligned for the search.

Sheridan meets with Franklin, Garibaldi, and Jacobs. Franklin treats Garibaldi's injury while Jacobs explains about the data crystal containing proof the President was not sick. Garibaldi explains that they will also take a sworn statement from the doctor in case anything else happens to him. Sheridan then explains that Cranston has figured out how to use the station's scanners to search for him – but he has a plan to hide Jacobs.

Hours later, Cranston, Sheridan, and Ivanova are in C'n'C, preparing to fire up the scanners. They get a request from Ambassador Kosh to disembark from the station, which they grant. The scanner fails to find a trace of the doctor on board. As Kosh's ship heads for the jumpgate, Cranston insists the station scan it for any life signs. One life sign is detected, but it is not human. The ship jumps through the gate. Cranston accepts that Jacobs is not on the station and prepares to leave.

After Cranston and his team are gone, the Vorlon ship returns to the station. Sheridan and his senior staff meet it in Bay 13. Sheridan explains that their scanners detecting "one lifeform" were detecting the ship itself: the ship is the product of organic technology. The ship then suddenly withdraws from itself the unconscious form of Dr. Jacobs and deposits him gently on the ground. Dr. Franklin then wakes him up, remarking that putting him in an artificially induced coma was the only way Kosh would agree to their plan. After he wakes up, Dr. Jacobs mentions that the ship "sang to him" while he was asleep.

Later, Sheridan turns over all the evidence he has to Sarah. While it is not enough to go public, it is a good start.

Garibaldi reminds Dr. Franklin that the last time he vouched for a doctor friend of his it resulted in "three dead bodies the station was trashed and an Ikarranwar machine was shooting at everything." referring to Dr. Vance Hendricks and the events of ("Infection").

In that episode, Hendricks mentioned the suspicion that the Vorlons had Organic Technology, a suspicion confirmed in this episode.

Sheridan mentions to Kosh how the Vorlon got inside his dream while he was captured, referencing his abduction by the Streib in "All Alone in the Night".

Cranston's reference to the station being able to locate an energy signature refers to the time Sheridan configured the scanners to locate Abel Horn, who also possessed an energy signature ("A Spider in the Web").

Garibaldi first suspected then Vice-President's story about being sick as phony as soon as he heard it, in ("Revelations").

Just before Sheridan notices the ribbon signal, a Ranger passes and climbs the stairs. Garibaldi recognizes him as a Ranger and turns, watching him leave the area.